Blasr

Blasr aligns Single Molecule Sequencing (SMS) reads to reference genomes to map long reads with high insertion and deletion error rates.

Key Features:

• Alignment efficiency and sensitivity: Efficiently maps high-throughput, long SMS reads (up to tens of kilobases) despite elevated insertion and deletion error rates.
• Successive Refinement Approach: Employs Basic Local Alignment with Successive Refinement (BLASR) to iteratively refine alignments for improved accuracy and speed.
• Combinatorial Model of Sequencing Error: Incorporates a combinatorial model of SMS sequencing errors to guide alignment scoring and tolerate insertions and deletions.

Scientific Applications:

• Bacterial genome mapping: Maps SMS reads from bacterial sequencing projects for genome characterization and analysis.
• Long-read genomic analyses: Maps long-read SMS data in complex organisms to enable genomic studies that leverage SMS technologies.

Methodology:

Performs iterative alignment refinement guided by a combinatorial model of sequencing error and was benchmarked on simulated reads and real data from a bacterial sequencing project.